1. Field of the Invention
The present invention generally relates to a method and a device for displaying a three-dimensional structure of a protein, and more particularly to a method for displaying a three-dimensional structure of a protein in which the three-dimensional structure of the protein is displayed in a graphic display or a character display.
2. Description of the Related Art
In the field of chemistry or physics, three-dimensional structures of various compounds are determined by using an X-ray diffraction crystal structure analysis or an NMR. The obtained data is stored in a database in order to support an analysis of the compound and production of a new compound. Protein Data Bank (PDB) is one of the most famous databases in which the stereo structures of the proteins obtained by the X-ray diffraction crystal structure analysis are stored. Also, Cambridge Structural Database (CSD) is widely known in which chemical compounds are registered.
The protein is a biopolymer in which a plurality of amino acids are bonded in a single chain in a primary structure. When the chain is folded to form a higher-order structure, various functions are revealed. Each amino acid of the protein is identified by a number resulting from numbering from an N-terminus to a C-terminus. The number is called an amino acid sequence number or an amino acid residue number. Each amino acid includes a plurality of atoms. Therefore, in the above PDB, a name of the protein, an identification number of the protein, amino acid numbers constituting the protein, atoms constituting the amino acids and a third-order coordinate of the atoms constituting the amino acids are included.
According to research, it has been found that the stereo structure (three-dimensional structure) of the compound is strongly related to the function thereof. In order to produce a new compound having a new function, a relationship between the stereo structure and the function has been studied through chemical experimentation. Between compounds having the same functions, a common specific structure is considered to influence the function of the compound. Thus, for the purpose described above, the screening of the compound having the specific structure is indispensable.
Japanese Laid-Open Patent Application 6-180737 discloses a device for displaying a stereo structure of a protein having a database in which stereo structure data of proteins are recorded. In this device, each amino acid constituting the protein is handled as a group of elements having a certain sequence, according to the database. When each group is related, a screening is performed based on a geometric relationship, a predetermined threshold or a function of the amino acid to find combinations satisfying the above requirement. Among the combinations, an amino acid sequence in which an average distance between each element is a minimum is found. After that, a position and a direction is determined so as to overlap the stereo structures of the protein.
In the preparation step of the overlapping of the stereo structure of the protein, a stereographic display of the protein structure data read from the database is conducted. Also, a character display of the protein structure data, in which each amino acid constituting the protein is represented by a character and the protein is displayed as a character line, is performed.
However, in the conventional method described above, the graphic display is not related to the character display. For example, when a certain range of amino acids is specified in the graphic display of the protein, the specified range of the amino acids is not defined in the character display. Thus, operational characteristics of the device are not adequate, especially for unskilled operators.